Site-directed pegylation of arginases and the use thereof as anti-cancer and anti-viral agents

ABSTRACT

The present invention provides a site-specific pegylated arginase conjugate and method for producing thereof. The site-specific pegylated arginase is homogeneous in molecular weight and shows therapeutic effect for treating cancers and viral infections. The method for producing the arginase conjugate comprises genetically modifying the gene encoding an arginase so that the PEG moiety can be attached to the enzyme at a predetermined, specific intended sites. This is achieved by removing the PEG-attaching amino acid residue(s) at undesirable site(s) while keeping or adding cysteine(s) at the desirable site(s) of the enzyme. Two exemplary embodiments of the pegylated arginase conjugate are directed to human arginase I (HAI) where a polyethylene glycol (PEG) moiety is site-specific covalently bonded to Cys 45  of the enzyme and  Bacillus caldovelox  arginase (BCA) where a polyethylene glycol (PEG) moiety is site-specific covalently bonded to Cys 161  of the enzyme.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a continuation-in-part application claiming benefit from U.S. Non-Provisional patent application Ser. No. 12/732,188 filed Mar. 26, 2010, which claims priority from U.S. Provisional Patent Application-No. 61/163,863 filed Mar. 26, 2009, and the content of which is incorporated herewith in its entirety by reference.

FIELD OF THE INVENTION

The present invention relates to the modification of an arginase for the purpose of increasing the enzyme's serum or circulating half-life and improving its pharmacokinetic properties, in vivo biological activity, stability, and reducing the immune reaction (immunogenicity) to the enzyme in vivo. More specifically, the present invention relates to a site-specific covalent conjugation of polyethylene glycol (PEG) to an arginase through genetically modifying the gene encoding the arginase to produce single or double site-specific pegylated arginase. These site-specific pegylated arginases become effective treatment means for a number of arginine-dependent diseases, such as, for example, various cancers and human immunodeficiency virus (HIV) infection.

BACKGROUND OF THE INVENTION Arginase

Arginase is a manganese metalloenzyme containing a metal-activated hydroxide ion, a critical nucleophile in metalloenzymes that catalyze hydrolysis or hydration reactions. Arginase converts naturally occurring arginine into ornithine and urea. The enzyme exits in many living organisms, including bacteria and humans (Jenkinson et al., 1996, Comp Biochem Physiol B Biochem Mol Biol, 114:107-32).

Pegylation of Arginase

Arginase may be used as a therapeutic agent and administered parenterally for various indications. However, parenterally administrated arginase, which is a protein, may be immunogenic and typically has a short pharmacological half-life. Consequently, it can be difficult to achieve therapeutically useful blood levels of the proteins in patients. These problems may be overcome by conjugating the proteins to polymers such as polyethylene glycol (PEG).

Covalent attachment of the inert, non-toxic, biodegradable polymer PEG, to molecules has important applications in biotechnology and medicine. Pegylation of biologically and pharmaceutically active proteins has been reported to improve pharmacokinetics, resulting in sustained duration, improve safety (e.g. lower toxicity, immunogenicity and antigenicity), increase efficacy, decrease dosing frequency, improve drug solubility and stability, reduce proteolysis, and facilitate controlled drug release (Roberts et al., 2002, Adv Drug Deliv Rev, 54:459-76; Harris & Chess, 2003, Nat Rev Drug Discov, 2:214-221).

PEG-protein conjugates produced by conventional methods in the art contain heterogeneous species, each being attached with a variable number of PEG molecules, ranging from zero to the number of amino groups that the protein has. Even for species that has the same number of PEG molecule attached, the site of attachment on the protein may vary from species to species. Such non-specific pegylation, however, can result in conjugates that are partially or virtually inactive. Reduction of activity may be caused by shielding the protein's active receptor binding domain when the PEG is attached at an improper site. Thus, there is a clear need for a better way of producing homogeneously pegylated protein molecules which retain the activity of the parent protein and making possible the administration of correct and consistent dosages necessary for clinical uses.

Cancer Treatment Via Amino Acid Deprivation

Amino acid deprivation therapy is an effective means for the treatment of some cancers. Although normal cells do not require arginine, many cancer cell lines are auxotrophic for this amino acid. Many lines of evidence have shown that in vitro arginine depletion, either with an arginine-degrading enzyme or by using an arginine-deficient medium, leads to rapid destruction of a wide range of cancer cells (Scott et al., 2000, Br J Cancer, 83:800-10). But direct use of enzymes, which are proteins, has problems of immunogenicity, antigenicity and short circulating half-life.

Inhibition of Virus by Arginine Deprivation

Viral infections are among the leading causes of death with millions of deaths each year being directly attributable to several viruses including hepatitis and human immunodeficiency virus (HIV). However, there are several problems with current anti-viral therapies. First, there are relatively few effective antiviral drugs. Many of the existing anti-viral agents cause adverse or undesirable side-effects. Most effective therapies (such as vaccination) are highly specific for only a single strain of virus. Frequently the virus undergoes mutation such that it becomes resistant to either the drug or vaccine. There is a need for methods for inhibiting viral replication which do not have the problems associated with the prior art.

Many studies over the last 30 years have demonstrated that extracellular arginine is required for viral replication in vitro. Historically this has been accomplished by making tissue culture media deficient in arginine and dialyzing the serum used as a supplement in order to achieve arginine free medium. Using this methodology to achieve arginine deprivation results in inhibition of replication of a large number of diverse families of viruses including: adenovirus (Rouse et al., 1963, Virology, 20:357-365), herpes virus (Tankersley, 1964, J Bacteriol, 87: 609-13).

Human Immunodeficiency Virus (HIV)

Acquired immune deficiency syndrome (AIDS) is a fatal disease, reported cases of which have increased dramatically within the past several years. The AIDS virus was first identified in 1983. It has been known by several names and acronyms. It is the third known T-lymphotropic virus (HTLV-III), and it has the capacity to replicate within cells of the immune system, causing profound cell destruction. The AIDS virus is a retrovirus, a virus that uses reverse transcriptase during replication. Two distinct families of HIV have been described to date, namely HIV-1 and HIV-2. The acronym “HIV” is used herein to refer to human immunodeficiency viruses generically. HIV replication is believed to be arginine-dependent, depletion of which would thus inhibit HIV replication.

SUMMARY OF THE INVENTION

According to the present invention, various native arginases are modified in order to promote attachment of a single or two PEG polymer(s). Although most proteins do not possess a specific native site or a free cysteine residue for the attachment of PEG polymer(s), the present invention has solved this problem by genetically engineering/mutating various arginase proteins to insert free cysteine residue(s) for site-directed mono- or double-pegylation. Alternatively, other arginase proteins may contain more free cysteine residues than desired or have one or more of them at undesirable positions. The present invention has solved this problem by genetically removing these free cysteine residues from the enzyme, leaving only the desirable site(s) for attachment of the PEG moiety.

Note that for both aspects of the present invention, site selection is carefully engineered to ensure that the attached PEG molecule does not interfere with the active binding site for the various arginases.

The selected pegylation sites are far away from the active binding site, and generally exposed to solvent to allow reaction with thiol-specific PEG molecules. To prevent disruption of tertiary structure or loss of protein structure, utilizing of the cysteine molecules involved in native disulfide bonds are avoided. Instead, novel “free” cysteine residues can be introduced/engineered or cysteine residues that are not involved in a disulfide bond can be used for thiol pegylation in arginases to avoid disulfide scrambling and protein misfolding.

In particular, an object of the present invention is to provide novel PEG-arginase conjugates substantially homogeneous and having PEG moiety covalently bound to specific sites at the arginase molecule. Two preferred embodiments of the present invention are Cys⁴⁵-human arginase I (HAI) and Cys¹⁶¹-Bacillus caldovelox arginase (BCA).

Another object of the present invention is to provide a method of producing site-directed, mono- or double-pegylated arginase conjugates, which have potent anti-cancer and anti-viral effects. One particular embodiment of the present invention comprises three general steps. The first step is a genetically modification of a gene encoding for an arginase so that the resulting arginase will have0 one to two free cysteine residue(s) so that the PEG moiety can attach to the enzyme at these specific intended site(s).

The second step is expressing the modified gene in a chosen system to produce desired arginase. The host where the modified gene is expressed may be human cells or tissues, or other organisms including, for example, a bacterial cell, a fungal cell, a plant cell, an animal cell, an insect cell, a yeast cell, or a transgenic animal. The third step is conjugation between the free cysteine residue(s) of the modified arginase and a maleimide group (MAL) of a PEG compound, resulting in a covalent bond between the PEG compound and the free cysteine(s) of the modified arginase.

Another object of the present invention is to provide a method of treating viral infection via arginine depletion. In one embodiment, the method of treatment employs homogeneous mono- or double-pegylated arginase to inhibit viruses' replication.

Another object of the present invention is to provide a method of treating and/or preventing replication of human immunodeficiency virus (HIV). In one embodiment, the method of treatment employs homogeneous mono- or double-pegylated arginase to inhibit HIV's replication.

Another object of the present invention is to provide a method of enhancing arginase's enzymatic activity by replacing the valine at position 20 of Bacillus caldovelox arginase (or the corresponding position in HAI and other arginases) with another amino acid residue, for example, proline.

Still another object of the present invention is to provide a method of enhancing arginase's enzymatic activity, which is accomplished by replacing the native metal cofactor manganese with cobalt.

The various features of novelty which characterize the present invention are pointed out with particularity in the claims annexed to and forming a part of this disclosure. For a better understanding of the present invention, its operating advantages, and specific objects attained by its use, reference should be made to the drawings and the following description in which there are illustrated and described preferred embodiments of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 shows (A) the nucleotide sequence of unmodified human arginase I (SEQ ID No: 1); (B) a mutated nucleotide sequence of the human arginase I designed for site-directed pegylation (SEQ ID No: 2) according to the present invention; (C) the nucleotide sequence of unmodified Bacillus caldovelox arginase (SEQ ID No: 3); and (D) a mutated nucleotide sequence of Bacillus caldovelox arginase designed for site-directed pegylation (SEQ ID No: 4) according to the present invention.

FIG. 2 shows (A) the amino acid sequence of the unmodified human arginase I (SEQ ID No: 5); (B) a modified amino acid sequence of human arginase I designed for Cys⁴⁵ site-directed pegylation (SEQ ID No: 6) according to the present invention; (C) the amino acid sequence of unmodified Bacillus caldovelox arginase (SEQ ID No: 7); and (D) a modified amino acid sequence of Bacillus caldovelox arginase designed for Cys¹⁶¹ site-directed pegylation (SEQ ID No: 8) according to the present invention.

FIG. 3 shows (A) the nucleotide and amino acid sequences of the human arginase I mutant (C168S/C303S) designed for Cys⁴⁵ site-directed pegylation (SEQ ID Nos: 9 and 10); (B) the alignment of the nucleotide and amino acid sequences of the 6×His-tagged human arginase I mutant (C168S/C303S) designed for-Cys⁴⁵ site-directed pegylation (SEQ ID Nos: 11 and 12); (C) the nucleotide and amino acid sequences of the Bacillus caldovelox arginase mutant (S161C) designed for Cys¹⁶¹ site-directed pegylation (SEQ ID Nos: 13 and 14); and (D) the alignment of the nucleotide and amino acid sequences of the 6×His-tagged Bacillus caldovelox arginase mutant (S161C) designed for Cys¹⁶¹ site-directed pegylation (SEQ ID Nos: 15 and 16), where the box close to the C-terminus represents the 6×His-tag encoding codons.

FIG. 4 shows (A) the crystal structure of the wild-type human arginase I (downloaded from NCBI website using Cn3D 4.1 software), showing that Cys⁴⁵ is far away from the active site; (B) the crystal structure of the wild-type Bacillus caldovelox arginase, showing that Ser¹⁶¹ is far away from the active site.

FIG. 5 shows (A) the conjugation procedures for Cys⁴⁵-specific mono-pegylation of the 6×His-tagged human arginase I mutant with a single chain mPEG-maleimide (20 kDa), showing that the double bond of a maleimide undergoes an alkylation reaction with a sulfhydryl group to form a stable thioether bond; and (B) the corresponding procedures for Cys¹⁶¹-specific mono-pegylation of the 6×His-tagged Bacillus caldovelox arginase mutant.

FIG. 6 depicts (A) a time-course for fermentation in a 2-liter fermenter by the E. coli BL21-DE3 containing the arginase gene, showing the results obtained from the batch fermentation and (B) the results obtained from the fed-batch fermentation; (C) the history plots of the batch fermentation and (D) the fed-batch fermentation, showing the changes of parameters such as temperature, stirring rate, pH, dissolved oxygen values; (E) the elution profile of the 6×His-tagged human arginase I mutant from a chelating FF sepharose column with the first peak being protein impurities and the second peak being the purified human arginase I; and (F) the elution profile of the 6×His-tagged Bacillus caldovelox arginase mutant from a chelating FF sepharose column with the first peak being the protein impurities and the second peak being the purified Bacillus caldovelox arginase.

FIG. 7 shows the SDS-PAGE analysis of different fractions involving (A) 6×His-tagged human arginase I mutant and (B) 6×His-tagged Bacillus caldovelox arginase mutant.

FIG. 8 shows (A) the SDS-PAGE analysis of the unpegylated human arginase I mutant and the Cys⁴⁵ pegylated human arginase I mutant (Lane 1: protein molecular weight marker; Lane 2: unpegylated human arginase I mutant; and Lane 3: Cys⁴⁵ pegylated human arginase I (HAI-PEG20)); (B) the SDS-PAGE analysis of unpegylated Bacillus caldovelox arginase mutant and the Cys¹⁶¹ pegylated Bacillus caldovelox arginase (Lane 1: protein molecular weight marker; Lane 2: the unpegylated Bacillus caldovelox arginase mutant; and Lane 3: Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20)).

FIG. 9 shows (A) the pharmacokinetic profiles of a single dose of non-pegylated and Cys⁴⁵ pegylated human arginase I (HAI-PEG20) injected intraperitoneally in BALB/c mice; and (B) the pharmacokinetic profiles of a single dose of non-pegylated and Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) injected intraperitoneally in BALB/c mice.

FIG. 10 shows (A) the pharmacodynamic profile of a single dose of Cys⁴⁵ pegylated human arginase I (HAI-PEG20) injected intraperitoneally in BALB/c mice up to Day 14; and (B) the pharmacodynamic profile of a single dose of Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) injected intraperitoneally in BALB/c mice up to Day 14.

FIG. 11 shows the average body weights (±s.e.m.) of different treatment groups:

(A) BALB/c nude mice xenografted with Hep3B human liver cancer cells injected with different drugs; (B) BALB/c nude mice xenografted with MCF-7 human breast cancer cells injected with Cys¹⁶¹ pegylated Bacillus caldovelox arginase; (C) BALB/c nude mice xenografted with A549 lung cancer cells injected with different drugs; and (D) BALB/c nude mice xenografted with HCT-15 colorectal cancer cells injected with different drugs, during the course of the study.

FIG. 12 shows (A) the in vivo activities (efficacies) of non-pegylated and Cys⁴⁵ pegylated human arginase I (HAI-PEG20) in BALB/c nude mice implanted with Hep3B human liver tumor cells subcutaneously, in terms of the tumor volume over the time course; (B) the in vivo activities of Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) in BALB/c nude mice xenografted with MCF-7 human breast cancer cells subcutaneously, in terms of the number of fold increase in the tumor volume over the time course; (C) the in vivo efficacies of Cys¹⁶¹ pegylated Bacillus caldovelox arginase in BALB/c nude mice bearing A549 lung cancer xenograft subcutaneously; (D) the in vivo efficacies of Cys¹⁶¹ pegylated Bacillus caldovelox arginase in BALB/c nude mice bearing A549 lung cancer xenograft subcutaneously (data are expressed as mean number of fold increase in tumor volume±s.e.m); (E) the in vivo efficacies of Cys¹⁶¹ pegylated Bacillus caldovelox arginase in BALB/c nude mice bearing HCT-15 colorectal cancer xenograft subcutaneously; and (F) the in vivo efficacies of Cys¹⁶¹ pegylated Bacillus caldovelox arginase in BALB/c nude mice bearing HCT-15 colorectal cancer xenograft subcutaneously (data are expressed as mean number of fold increase in tumor volume±s.e.m.).

FIG. 13 shows an HIV inhibition assay for Cys⁴⁵ pegylated human arginase I (HAI-PEG20).

FIG. 14 shows the HIV inhibition assay for azido-thymidine (AZT).

FIG. 15 shows the cytotoxicity of Cys⁴⁵ pegylated human arginase I (HAI-PEG20) in H9 cells inoculated with HIV strain RF.

FIG. 16 shows a comparison of steady-state kinetics of human arginase I with different metal cofactors, i.e., Mn²⁺ and Co²⁺.

FIG. 17 shows a comparison of steady-state kinetics of the V20P mutant of Cys¹⁶¹ Bacillus caldovelox arginase (BCA mutant V20P) and the Cys¹⁶¹ Bacillus caldovelox arginase (BCA) substituted with Mn²⁺ or Co²⁺.

FIG. 18 illustrates a hypothesis and working model for cancer cells that are OTC-negative.

FIG. 19 shows the alignment of certain residues in arginases across various species: (A) Group 1 organisms that possess cysteine equivalent to Cys-45 in human arginase; (B) Group 2 organisms that possess Serine equivalent to Ser-161 in Bacillus caldovelox arginase; (C) Group 3 organisms that possess two cysteines equivalent to Cys-45 and Cys-168 of human arginase; (D) Group 4 organisms that possess Tyrosine and Serine equivalent to Tyr-41 and Ser-161 of Bacillus caldovelox arginase.

FIG. 20 shows (A) the locations of Ser-161 within the three-dimensional structure of Bacillus caldovelox arginase; (B) its equivalent position Cys-168 within human arginase and (C) their overlay view.

FIG. 21 shows (A) the locations of Cys-45 within the three-dimensional structure of human arginase; (B) its equivalent position Tyr-41 within Bacillus caldovelox arginase and (C) their overlay view.

FIG. 22 depicts lysine positions on Bacillus caldovelox arginase.

FIG. 23 shows the SDS-PAGE analysis of the unpegylated BCA mutant V20P and the Cys¹⁶¹ pegylated BCA mutant V20P (Lane 1: protein molecular weight marker; Lane 2: unpegylated BCA mutant V20P; and Lane 3: Cys¹⁶¹ pegylated BCA mutant V20P).

DETAILED DESCRIPTION OF THE INVENTION

According to the present invention, site-specific pegylation of various arginases can be controlled by controlling the availability of sites where pegylation can occur. These sites are selected such that the pegylation does not block the active bonding site while retaining the arginase activity. Although typically a single site is provided for pegylation, more than one carefully engineered site can be provided depending upon the species of arginase.

Further, the present inventors have determined that alignment of human and Bacillus caldovelox arginase sequences with sequences from other species revealed a high degree of conservation across many species in the regions where successful pegylation has been performed in human and Bacillus caldovelox arginases (FIGS. 19, 20, 21 and 22). For those arginase sequences that possess an equivalent of Cys-45 (found in human arginase) or Ser-161 (found in Bacillus caldovelox arginase), it is determined that the site-specific arginase pegylation for human arginase or Bacillus caldovelox arginase can be extended to those additional species. Thus, as discussed below, those additional species are genetically engineered for the site-specific pegylation as described below for the human arginase and Bacillus caldovelox arginase.

Cloning of Human Arginase I Gene (HAI)

The gene sequence of human arginase I is shown in FIG. 1A (SEQ ID No: 1). The encoding gene for 6×His-tagged human arginase I (HAI) is generated by polymerase chain reaction (PCR) from the pAED4/HAI plasmid using the following oligonucleotides to generate an NdeI site at 5′-end and BamHI site at 3′-end. Primer HuAr07-F: 5′ GAT.ATA.CAT.ATG.CAT.CAC.CAT.CAC 3′ (SEQ ID NO: 17) and Primer HuAr08-R: 5′ AGT.GCA.GGA.TCC.TTA.CTT.AGG.TGG.GTT.AAG.GTA.GTC 3′ (SEQ ID NO: 18). The PCR product is cut with NdeI and BamHI and subcloned into pET3a expression plasmid vector (Strategene).

The pET3a E. coli expression plasmid vector contains a T7 promoter. The T7 promoter is positioned upstream from the gene 10 leader fragment. The correct sequence is confirmed by DNA sequencing the entire coding region for human arginase I (FIG. 1A). This plasmid is referred to as pET3a/HAI.

Cloning of Bacillus caldovelox Arginase Gene (BCA)

The gene sequence of Bacillus caldovelox arginase is shown in FIG. 1C (SEQ ID No: 3). The encoding gene for 6×His-tagged Bacillus caldovelox arginase (BCA) is cut from the pUC57/BCA plasmid using NdeI and BamHI restriction enzymes. The insert fragment is subcloned into pET3a expression plasmid vector (Strategene).

The correct sequence is confirmed by sequencing the entire coding region for Bacillus caldovelox arginase (FIG. 1C). This plasmid is referred to as pET3a/BCA.

Mutagenesis of HAI

The plasmid pET3a/HAI is used as a template for site-directed mutagenesis according to the QuikChange® site-directed mutagenesis kit (Strategene). The codons for Cys¹⁶⁸ and Cys³⁰³ residues are mutated to the codons for Ser¹⁶⁸ and Ser³⁰³ respectively using the following pairs of mutagenic primers (SEQ ID No: 19, 20, 21, and 22, respectively):

Codon for Cys¹⁶⁸ being mutated to codon for Ser¹⁶⁸:

Primer HuAr01-F: (SEQ ID No. 19) 5′ GGG.TGA.CTC.CCT.CTA.TAT.CTG.CCA.AGG 3′; Primer HuAr02-R: (SEQ ID No. 20) 5′ CCT.TGG.CAG.ATA.TAG.AGG.GAG.TCA.CCC 3′; and Codon for Cys³⁰³ being mutated to codon for Ser³⁰³:

Primer HuAr03-F: (SEQ ID No. 21) 5′ GCA.ATA.ACC.TTG.GCT.TCT.TTC.GGA.CTT.GC 3′; Primer HuAr04-R: (SEQ ID No. 22) 5′ GCA.AGT.CCG.AAA.GAA.GCC.AAG.GTT.ATT.GC 3′.

The mutated plasmid according to the above mutagenesis schemes is transformed firstly into competent E. coli Top 10 cells. The gene sequence of the mutated plasmid is confirmed by DNA sequencing. The gene sequence of HAI mutant designed for Cys⁴⁵ site-directed pegylation is shown in FIG. 1B (SEQ ID No: 2). The mutated plasmid is then transformed into E. coli BL21-DE3 cells for protein expression. The amino acid sequence of the wild-type HAI is shown in FIG. 2A (SEQ ID No: 5). The amino acid sequence of the C168S/C303S mutant is shown in FIG. 2B (SEQ ID No: 6), FIG. 3A (SEQ ID No: 10) and FIG. 3B (SEQ ID No: 12). As shown in FIG. 2B, two cysteine residues in the wild-type human arginase I are replaced by serine residues. These two serine residues are underlined in FIG. 2B. The only cysteine residue present after the replacement is Cys45. This HAI mutant is called C168S/C303S, which only contains one single cysteine residue (also underlined in FIG. 2B). Crystal structure of the wild-type HAI is shown in FIG. 4A. Based on this structure, the rational protein drug design for constructing the C168S/C303S mutant is made. In FIG. 2D, it is shown that only one serine residue in Bacillus caldovelox arginase is replaced by a cysteine residue. This cysteine residue is underlined in FIG. 2D. The 6×His-tag region is also underlined and located at the C terminus. This mutant is called S161C.

Expression and Purification of 6×His-Tagged Arginases

E. coli BL21-DE3 harboring the plasmid containing a mutated arginase gene encoding 6×His-tagged human arginase I are grown overnight at 37° C. in LB medium containing 80 μg/mL ampicillin. The inoculum is diluted at 1:25 and grown to OD600˜0.8 in a shake flask or diluted at 1:10 and grown to OD600˜15 in a fermenter. The cells are then induced with 0.4 mM IPTG for 4 hours. The bacterial cells are collected by centrifugation, followed by resuspension in 50 mM Tris, 0.1 M NaCl, 10 mM MnCl₂, pH 7.4, and then disrupted by high pressure homogenization.

The 6×His-tagged human arginase I is purified by a chelating FF sepharose (GE Healthcare) column (5.0 cm×9 cm; bed volume of 176 mL) equilibrated with Buffer A (0.02 M sodium phosphate, 0.5 M NaCl, pH 7.4). The 6×His-tagged arginase is eluted with a gradient of 0.15 to 0.25 M imidazole (FIG. 6E & FIG. 6F). The flow rate is 20 mL/min. The fractions (FIG. 7A & FIG. 7B) containing purified arginase are collected. The yields of purified arginase are about 280 mg/L cell cultures.

The same procedure as described above for 6×His-tagged human arginase I is also used to obtain purified 6×His-tagged Bacillus caldovelox arginase in the present invention.

Site-Directed Pegylation of 6×His-Tagged Arginases

FIG. 5A shows the procedures for conjugating Cys⁴⁵-specific mono-pegylation of the 6×His-tagged human arginase I mutant with a single chain mPEG-maleimide (20 kDa), referred to as “HAI-PEG20”. The double bond of a maleimide undergoes an alkylation reaction with a sulfhydryl group to form a stable thioether bond. FIG. 5B shows the conjugation procedures for Cys¹⁶¹-specific mono-pegylation of the 6×His-tagged Bacillus caldovelox arginase mutant with a single chain mPEG-maleimide (20 kDa), referred to as “BCA-PEG20”. One gram of 6×His-tagged arginase is diafiltered into 0.02 M sodium phosphate, 0.5 M NaCl, pH 7.4, using Millipore Tangential Flow Filtration system (500 mL) with 10 K (cut-off) membrane (Millipore). The concentration of arginase is finally diluted to about 2 mg/mL. The reducing agent Tris(2-carboxyethyl)phosphine, TCEP, is added in a molar excess of 10 moles to one mole of arginase for reduction and the solution is gently stirred for 4 hours at room temperature. mPEG-Maleimide or mPEG-MAL (20 kDa) (Sunbright) in a molar excess of 20 moles to one mole of arginase is added to the reduced arginase and stirred for overnight at 4° C.

The progress of site-directed pegylation is monitored by SDS-PAGE (FIGS. 8A & 8B). Under the above described conditions, the free sulfhydryl group of cysteine at position 45 on human arginase I is specifically linked via a stable thioether bond to the activated maleimide group of mPEG-MAL (20 kDa). The final product of conjugation comprises predominantly Cys⁴⁵ pegylated human arginase I, unconjugated human arginase I, and mPEG-MAL (20 kDa). Similarly for Bacillus caldovelox arginase, the cysteine residue at position 161 is specifically linked via a stable thioether bond to the activated maleimide group of mPEG-MAL (20 kDa).

The mPEG-MAL (20 kDa) pegylated arginase is advantageous over the mPEG-MAL (5 kDa) pegylated arginase in terms of a longer half-time, and advantageous over the mPEG-MAL (40 kDa) pegylated arginase in terms of a better solubility.

Batch Fermentation in a 2-Liter Fermenter

The E. coli BL21-DE3 strain containing the arginase gene is stored at −80° C. To prepare the seed inoculum for batch and fed-batch fermentation, 100 μL frozen stock of the aforementioned strain are transferred into 250 mL flask containing 80 mL of fermentation medium. The bacterial culture is cultivated at 37° C. and pH 7.0 in an orbital shaker rotating at 250 rpm. The cultivation is terminated when OD600 nm reaches 5.5-6.0 at about 8-10 hours. The 12 mL (1%) seed inoculum is introduced into the 2-L fermenter containing 1,200 mL autoclaved enriched fermentation medium. The batch fermentation is carried out at a temperature of 37° C. The pH is maintained at 7.0 by adding sodium hydroxide and hydrochloric acid. The dissolved oxygen level is controlled at above 30% air saturation by introducing air at 1-4 L/min and adjusting the stirring rate of the fermenter at 300-1,200 rpm. Isopropyl-beta-D-thiogalacto-P (IPTG) 100 mM, inducer of the protein expression of Bacillus caldovelox arginase (BCA), is introduced into the fermentation broth to a final concentration of 0.5 mM when the OD600 nm is about 11.0 at 5 hours. After the IPTG induction, the fermentation continues until about 9 hours when the OD600 nm is about 16.4. The fermentation cells are harvested for separation and purification of BCA at about 4 hours after IPTG induction. The aforementioned strain produces active BCA in an amount of about 105 mg/L of the fermentation medium. The time-course of the fermentation is plotted in FIG. 6A. The history plot of this batch fermentation showing the changes of parameters such as temperature, stirring rate, pH and dissolved oxygen values is depicted in FIG. 6C.

Fed-Batch Fermentation in a 2-L Fermenter

The Fed-batch fermentation with high cell density culture is carried out at 37° C., pH 7.0 and dissolved oxygen is kept above 30% air saturation during the whole fermentation process. The procedure for preparing the seed inoculum is similar to that of the batch fermentation described above. The fermentation is initially started with batch cultivation strategy by introducing 5 mL (1%) seed inoculum into the 2-L fermenter containing 500 mL autoclaved enriched fermentation medium. The dissolved oxygen decreases gradually to around 30% air saturation during the growth phase in batch cultivation period. Once the dissolved oxygen level increases to above 80%, representing the depletion of carbon source, the PO₂ stat fed-batch strategy is started with the addition of feeding the enriched medium. In this strategy, the feeding rate is adjusted to maintain the dissolved oxygen level of below 60%, which provides minimal but adequate amount of carbon source during fermentation process. Isopropyl-beta-D-thiogalacto-P (IPTG) 100 mM is introduced into the fermentation broth to a final concentration of 0.5 mM when the OD600 nm is about 100 at 18 hours. After the IPTG induction, the fermentation continues until about 28 hours when the OD600 nm is about 186.8. The fermentation cells are harvested for separation and purification of BCA at about 10 hours after IPTG induction. The aforementioned strain produces active BCA in an amount of about 1,489.6 mg/L of the fermentation medium, which is higher than all the other reported yields of different types of arginase. The time-course of the fermentation is plotted in FIG. 6B. The history plot of this fed-batch fermentation showing the changes of parameters such as temperature, stirring rate, pH and dissolved oxygen values is depicted in FIG. 6D.

Comparison of Batch and Fed-Batch Fermentation

Table 1 below compares the results of batch and fed-batch fermentation. The comparison demonstrates that the fed-batch fermentation is much superior to the batch operation in terms of culture OD600, cell dry weight and yield of arginase per liter culture.

TABLE 1 Batch fermentation Fed-batch fermentation Maximum OD₆₀₀ reached 16.4 186.8 Cell dry weight (g) 4.9 76.6 yield of BCA (mg/L) 105.0 1489.6 yield of BCA (mg/g-cell) 21.4 19.4

Purification of Site-Directed Pegylated Arginases

Affinity nickel ion column chromatography is used to separate 6×His-tagged site-directed pegylated arginases from mPEG-MAL (20 kDa) as described as follows. The final products of conjugation are loaded onto a chelating FF sepharose (GE Healthcare) column (5.0 cm×9 cm; bed volume of 176 mL) equilibrated with Buffer A (0.02 M sodium phosphate, 0.5 M NaCl, pH 7.4). The column is washed with 5 column volumes of Buffer A to remove free mPEG-MAL (20 kDa). The pegylated arginase is eluted using a salt gradient from 30% to 100% of Buffer B (0.02 M sodium phosphate, 0.5 M NaCl, 0.5 M imidazole, pH 7.4) for 5 column volumes. The protein content of the eluent is monitored at 280 nm wavelength. The column is eluted at a flow rate of 20 mL/min and the pegylated arginase fractions are collected. The pooled fractions are diafiltered into PBS buffer (Gibco) and concentrated to 4-6 mg/mL. Before animal study, the endotoxin in the protein drug is removed using a Q-filter (Sartoris).

Site-specific Pegylation at Position Equivalent to Cys-45 of Human Arginase (HAI)

As seen in FIG. 19A, Capra hircus arginase I, Heterocephalus glaber arginase I, Bos taurus arginase I, Sus scrofa arginase I, Plecoglossus altivelis arginase I, Salmo salar arginase I, Oncorhynchus mykiss arginase I, Osmerus mordax arginase I, Hyriopsis cumingii arginase I, Rattus norvegicus arginase II, Mus musculus arginase II, human arginase II, Bos taurus arginase II, Heterocephalus glaber arginase II, Pan troglodytes arginase II, Oryctolagus cuniculus arginase II, Delftia arginase, Bacillus coagulans arginase, Hoeflea phototrophica arginase and Roseiflexus castenholzii arginase possess an equivalent of Cys-45, analogous to the human arginase described above. Using procedures similar to those described above, cysteine residue at position equivalent to Cys-45 can be used and site-specific pegylation can be performed on that site.

Site-Specific Pegylation at Position Equivalent to Ser-161 of Bacillus caldovelox Arginase (BCA)

Further, as seen in FIG. 19B, the serine residue of arginases of Bacillus methanolicus, Bacillus sp. NRRL B-14911, Planococcus donghaensis, Paenibacillus dendritiformis, Desmospora sp., Methylobacter tundripaludum, Stenotrophomonas sp., Microbacterium laevaniformans, Porphyromonas uenonis, Agrobacterium sp., Octadecabacter arcticus, Agrobacterium tumefaciens, Anoxybacillus flavithermus, Bacillus pumilus, Geobacillus thermoglucosidasius, Geobacillus thermoglucosidans, Brevibacillus laterosporus, Desulfotomaculum ruminis, Geobacillus kaustophilus, Geobacillus thermoleovorans, Geobacillus thermodenitrificans, Staphylococcus aureus, Halophilic archaeon DL31, Halopiger xanaduensis and Natrialba magadii, analogous to Ser-161 of BCA, can be engineered to be a cysteine residue. As set forth above, this creates a site-specific pegylation location in these arginases that can be fabricated according to the above techniques.

Additional Pegylation Sites in Human and Bacillus caldovelox Arginases

Additional sites have been identified for site-specific pegylation of human and B. caldovelox arginase that do not interfere with the active site of the respective arginases. As seen in FIG. 20, in human arginase, position 168 is substantially equivalent to Ser-161 of B. caldovelox arginase. Further, as seen in FIG. 21, in B. caldovelox arginase, position 41 can be used for site-specific pegylation (equivalent site of Cys-45 of human arginase I). Though the two enzymes do not share exactly the same amino acid at the position, given the resembling features of the amino acid side chain (human Cys-168 and B. caldovelox Ser-161 are both polar side chains, and human Cys-45 and B. caldovelox Tyr-41 both have bulky side chains), and the highly similar 3-dimensional structures of the 2 arginases, the results in one enzyme can be extended to the other.

Site-specific Single Pegylation for Human and Bacillus caldovelox Arginases at Additional Site

Based on the highly similar 3-dimensional structures of BCA and HAI it can be inferred reasonably that the results in BCA can be extrapolated to HAI, indicating that Cys-168 would be a favourable site for PEG attachment far away from the enzyme active site. In this case, Cys-45 and Cys-303 would be substituted with serine to ensure specific attachment of PEG at Cys-168. Conversely, Tyr-41 of BCA can be engineered to a cysteine for site-specific PEG attachment.

Site-Specific Pegylation at Two Sites in Human and Bacillus caldovelox Arginases

Further to the discussion above, the present invention can also perform site-specific pegylation at two sites on human arginase and at two sites on B. caldovelox arginase. That is, the human arginase can be pegylated at position 45 and position 168 while B. caldovelox arginase can be pegylated at sites 41 and 161.

Site-Specific Pegylation at Two Sites Equivalent to Cys-45 and Cys-168 of Human Arginase

As shown in FIG. 19C, arginases from organisms (Capra hircus arginase I, Heterocephalus glaber arginase I, Bos taurus arginase I, Sus scrofa arginase I, Plecoglossus altivelis arginase I, Salmo salar arginase I, Oncorhynchus mykiss arginase I, Osmerus mordax arginase I, Hyriopsis cumingii arginase I, Rattus norvegicus arginase II, Mus musculus arginase II, human arginase II, Bos taurus arginase II, Heterocephalus glaber arginase II, Pan troglodytes arginase II, Oryctolagus cuniculus arginase II) possess two cysteine residues equivalent to Cys-45 and Cys-168 of HAI, which can be used for site-specific pegylation at two sites. Other redundant cysteines in these proteins (e.g. Cys-303 of HAI) will be specifically engineered as serine instead.

Site-Specific Pegylation at Two Sites Equivalent to Tyr-41 and Ser-161 of Bacillus caldovelox Arginase

As shown in FIG. 19D, arginases of organisms (Bacillus methanolicus, Desmospora sp., Geobacillus thermoglucosidasius, Geobacillus thermoglucosidans, Brevibacillus laterosporus, Geobacillus kaustophilus, Geobacillus thermoleovorans, Geobacillus thermodenitrificans) possess Tyrosine and Serine equivalent to Tyr-41 and Ser-161 of BCA, which can both be engineered into cysteines for site-specific pegylation at two sites.

Pegylation at Lysine Residues in Bacillus caldovelox Arginase

As seen in FIG. 22, various lysine residues (14 shown in FIG. 22) present in B. caldovelox arginase are spaced at positions away from the active site and can serve as site-specific pegylation locations.

In Vitro Cytotoxicity of Site-Directed Pegylated Arginases

In vitro cytotoxicity of Cys⁴⁵ pegylated human arginase I and Cys¹⁶¹ pegylated Bacillus caldovelox arginase are studied by standard MTT assay in different human cancer cells (melanoma, hepatocellular carcinoma, gastric adenocarcinoma, colorectal adenocarcinoma, pancreatic carcinoma, pancreatic adenocarcinoma, and T cell leukaemia)

The known numbers of cells (5000) are incubated for 68 hours in each well of 96-well plate in a 5% CO₂ incubator at 37° C. in the presence of different concentrations of Cys⁴⁵ pegylated human arginase I and Cys¹⁶¹ pegylated Bacillus caldovelox arginase. After 68 hours of drug incubation, 50 μg of the MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, a tetrazole) solution is added in each well and incubated for another 4 hours. The supernatant is discarded and 100 μL of 10% SDS/0.01 M HCl is added in each well and then incubated overnight. The absorbance is recorded at 540 nm by a microplate reader (Bio-Rad). The concentration of each drug required to inhibit the 50% cell growth (IC₅₀) is determined for different cancer cell lines. Experiment is performed in triplicate.

The IC₅₀ values of Cys⁴⁵ pegylated human arginase I (HAI-PEG20) and Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) for different cell lines are calculated and the results are listed in Table 2. As Bacillus caldovelox arginase is never known for anti-cancer response, it is thus the first time to have demonstrated its anti-cancer properties and efficacies. In various melanoma cell lines (SK-MEL-2, SK-MEL-28, A375), the IC₅₀ values of Cys⁴⁵ pegylated human arginase I are lower when compared to those of Cys¹⁶¹ pegylated Bacillus caldovelox arginase. Among different hepatocellular carcinoma cell lines (HepG2, Hep3B, PLC/PRF/5), HepG2 cells are the most sensitive to both Cys⁴⁵ pegylated human arginase I and Cys¹⁶¹ pegylated Bacillus caldovelox arginase. Taken together, all liver cancer (HCC) and melanoma cell lines tested are inhibited efficiently by BCA-PEG20 and HAI-PEG20.

Cys¹⁶¹ pegylated Bacillus caldovelox arginase is also tested for the other five cancer cell lines including gastric adenocarcinoma, colorectal adenocarcinoma, pancreatic carcinoma, pancreatic adenocarcinoma, and T cell leukaemia. For gastric adenocarcinoma cell lines, the IC₅₀ of Cys¹⁶¹ pegylated Bacillus caldovelox arginase for MKN-45 cells (0.798 U/mL) is similar to that for AGS cells (0.662 U/mL). Among different colorectal adenocarcinoma cell lines (WiDr, HT-29, SW1116), WiDr cells and HT-29 cells are more sensitive to Cys¹⁶¹ pegylated Bacillus caldovelox arginase. When comparing the pancreatic carcinoma cell line (PANC-1) and the pancreatic adenocarcinoma cell line (BxPC-3), the IC₅₀ of Cys¹⁶¹ pegylated Bacillus caldovelox arginase is lower in PANC-1 cells by four-fold. For T cell leukaemia cell line (Jurkat, Clone E6-1), the IC₅₀ of Cys¹⁶¹ pegylated Bacillus caldovelox arginase (0.41 U/mL) is also relatively low when compared to the other cancer cell lines. Taken together, all cancer cell lines tested are sensitive to (and inhibited by) HAI-PEG20 and BCA-PEG20 treatments.

TABLE 2 In vitro IC₅₀ Cys¹⁶¹ pegylated Bacillus Cys⁴⁵ pegylated caldovelox human arginase I arginase Tumor Cell line U/mL μg/mL U/mL μg/mL Melanoma SK-MEL-2 0.079 0.80 0.612 11.25 SK-MEL-28 0.064 0.65 0.910 16.72 A375 0.088 0.90 0.15 2.76 Hepatocellular HepG2 0.097 0.99 2.002 36.79 carcinoma Hep3B 0.290 2.95 9.1 57.68 PLC/PRF/5 0.94  9.56 2.376 43.67 Gastric MKN-45 — 0.798 14.67 adenocarcinoma AGS — 0.662 12.17 Colorectal WiDr 0.075 0.76 0.192 3.53 adenocarcinoma HT-29 — 0.220 4.04 SW1116 0.41  4.18 1.515 27.84 Pancreatic PANC-1 — 0.263 4.84 carcinoma Pancreatic BxPC-3 — 0.846 15.54 adenocarcinoma T cell leukemia Jurkat, Clone — 0.410 7.54 E6-1

Depletion of Arginine by Site-Directed Pegylated Arginases

Pharmacodynamics of Cys⁴⁵ pegylated human arginase I and Cys¹⁶¹ pegylated Bacillus caldovelox arginase are studied using BALB/c normal mice. The study is carried out in conjunction with the pharmacokinetic study (described below). Therefore, the protocol remained the same. Again, the blood samples collected are centrifuged immediately at 13,200 rpm for 5 minutes and the plasma layer are collected for further analysis using the Amino Acid Analyzer (Biochrom 30, Biochrom Ltd., England). For pharmacokinetic study, plasma samples are first purified from urea using molecular sieve centrifugal filter units as sample preparation columns before subjecting to enzymatic activity determinations.

As shown in FIG. 10A, ornithine level starts to increase after the injection of Cys⁴⁵ pegylated human arginase I (HAI-PEG20) and stays at a high level (>150 μM) up to Day 3. Arginine is totally depleted starting from 6 hour (Day 0) and starts to appear 6.8±2.3 days after arginase administration. This indicates that HAI-PEG20 depletes blood arginine efficiently.

For Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20), ornithine level also starts to increase and stays at a high level (>170 μM) up to Day 3 (FIG. 10B). Arginine is totally depleted starting from 6 hour (Day 0) and starts to appear 6.7±2.1 days after arginase administration. This indicates that BCA-PEG20 depletes blood arginine efficiently. Both pegylated arginases (Cys⁴⁵ pegylated human arginase I and Cys¹⁶¹ pegylated Bacillus caldovelox arginase) display a similar pharmacodynamic profile.

As shown in FIG. 9A, the enzymatic activity of Cys⁴⁵ pegylated human arginase I increases sharply 6 hours after drug administration representing a very fast drug absorption and provides significantly higher drug exposure to the animal as presents by an increase in area under curve for over 3.8 folds in comparison to the unpegylated human arginase I. For Cys¹⁶¹ pegylated Bacillus caldovelox arginase, plasma drug arginase activity increases sharply 6 hours after drug administration representing a very fast drug absorption follows by a slow drug elimination with a terminal half-life of 83.7±24.4 hours (FIG. 9B). In comparison to unpegylated Bacillus caldovelox arginase that has a drug elimination half-life of about 7.3±2.3 hours, Cys¹⁶¹ pegylated Bacillus caldovelox arginase has shown excellent improvement in extension of drug elimination half-life for over 11 folds.

In Vivo Anti-Tumor Efficacy on Liver Cancer

In vivo anti-tumor efficacy of non-pegylated human arginase I (HAI) and Cys⁴⁵ pegylated human arginase I (HAI-PEG20) on liver cancer are studied and compared.

A number of BALB/c nude mice are injected with hepatocellular carcinoma Hep3B cells intraperitoneally (i.p.) and maintained in vivo. Then each of the 30 BALB/c nude mice is injected with about 1×10⁶ of the in vivo maintained cancer cells to the right axilla subcutaneously. When palpable tumors of about 5 mm in diameter are found, the mice are separated into three different groups (see Table 3). Drugs or PBS buffer are administered intraperitoneally weekly for 8 weeks. Body weights and tumor dimensions (L: length of the longer diameter and W: length of the shorter diameter of the tumor) are measured twice a week. Tumor volume (½×L×W²) is calculated and plotted against the time of incubation. After 60 days or when tumor diameter reaches about 2.5 cm, the mice are euthanized. Survival rates of the mice are recorded at the end of the study.

TABLE 3 In vivo anti-tumor activity protocol Units/ Group Testing drug Mice mouse Route 1 PBS 5M5F n/a i.p. 2 Non-pegylated human arginase I 5M5F 500 i.p. 3 Cys⁴⁵ pegylated human arginase I 5M5F 500 i.p.

As shown in FIG. 11A, the average body weights of the PBS control group, the Cys⁴⁵ pegylated human arginase I group, and the non-pegylated human arginase I group are 25.9±0.2 g, 25.0±0.2 g, and 25.5±0.2 g respectively, with no significant change throughout the experiment for each group.

In terms of the tumor volume, Cys⁴⁵ pegylated human arginase I (HAI-PEG20) significantly reduces the rate of tumor growth starting from Day 47 compared to the PBS control group (p<0.01); while non-pegylated human arginase I (HAI) does not show any significant effect (p>0.05) (FIG. 12A).

In Vivo Anti-Tumor Efficacy on Breast Cancer

In vivo anti-tumor efficacy of Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) on breast cancer is determined next.

Athymic nude BALB/c mice (age of 6-8 weeks) are housed under sterile conditions with 12 hour light-dark cycle and provided with autoclaved feed ad libitum. The mice are acclimated for at least 1 week before the start of experiments. Each nude mouse is injected with 1×10⁶ MCF-7 human breast cancer cells to the right axilla subcutaneously. When palpable tumors of 5 mm diameter are found, the mice are randomly separated into two different groups (Table 4). Drugs or control vehicle (PBS) are injected intraperitoneally once per week starting from Day 0 for 18 days. Tumor dimensions (L: longest diameter and W: its perpendicular diameter) and body weights are measured on every Mondays, Wednesdays and Fridays with Vernier caliper. Tumor volume is calculated with the formula (½×L×W²) and number of fold increase in tumor volume is calculated with reference to Day 0. The results are plotted against time. At Day 18 or when tumor diameter reaches 2.5 cm, the mice are euthanized and the final tumor and body weight are recorded.

TABLE 4 In vivo anti-tumor activity protocol Group Testing drug Units/mouse route Mice 1 PBS (control) N/A i.p. 4M 4F 2 Cys¹⁶¹-pegylated Bacillus 250 i.p. 4M 4F caldovelox arginase

As shown in FIG. 11B, no significant difference in average body weights of the control group (18.76±0.50) and Cys¹⁶¹-pegylated Bacillus caldovelox arginase (19.76±0.66) is observed throughout the experiment. Cys¹⁶¹-pegylated Bacillus caldovelox arginase significantly suppresses tumor growth and reduces the number of fold increase in tumor volume in comparison to the PBS control group (2-way ANOVA: p<0.0001, FIG. 12B). Using Bonferroni post-test, the reduction is statistically significant starting from Day 15 (p<0.01) where the reduction is over 2.8 folds.

In Vivo Anti-Tumor Efficacy on Lung Cancer

Athymic nude BALB/c mice (age of 6-8 weeks) are housed under sterile conditions with 12 hour light-dark cycle and provided with autoclaved feed ad libitum. The mice are acclimated for at least 1 week before the start of experiments. Each nude mouse is injected with 5×10⁶ A549 human lung cancer cells to the right axilla subcutaneously with matrigel growth supplement. When palpable tumors of about 5 mm diameter are found, the mice are randomly separated into three different groups (Table 5). Drugs or control vehicle (PBS) are injected intraperitoneally once per week starting from Day 0. Tumor dimensions (L: longest diameter and W: its perpendicular diameter) and body weights are measured on every Monday, Wednesday and Friday with Vernier caliper. Tumor volume is calculated with the formula (½×L×W²) and number of fold increase in tumor volume (relative tumor volume) is calculated with reference to Day 0.

TABLE 5 In vivo anti-tumor activity protocol Group Testing drug Units/mouse route Mice 1 PBS (control) N/A i.p. 5M 5F 2 Unpegylated Bacillus caldovelox 250 i.p. 5M 5F arginase 3 Cys¹⁶¹-pegylated Bacillus 250 i.p. 5M 5F caldovelox arginase

No significant difference in average body weights between different groups is observed throughout the experiment and last recorded as 23.98±2.68 g for the control group, 23.68±1.50 g for the unpegylated Bacillus caldovelox arginase and 23.16±2.08 g for the Cys¹⁶¹-pegylated Bacillus caldovelox arginase at the end of experiment (FIG. 11C).

Cys¹⁶¹-pegylated Bacillus caldovelox arginase (BCA-PEG20) however suppresses tumor growth significantly and statistically in comparison to vehicle control group in terms of progressive changes of tumor volume (FIG. 12C) and number of folds of tumor volume (FIG. 12D). Two-way ANOVA shows p values at <0.0001 for both parameters while Bonferroni post-test indicates the difference to start from Day 28 (p<0.05) to Day 35 (p<0.001) for tumor volume and from Day 30 to Day 35 (p<0.01 for all points) for relative tumor volume. The unpegylated Bacillus caldovelox arginase (BCA) at the same dose regime also shows anti-lung cancer effects in a similar extent with statistical significance for both parameters (two-way ANOVA, both with p<0.0001).

In Vivo Anti-Tumor Efficacy on Colorectal Cancer

In vivo anti-tumor efficacy of unpegylated (BCA) and Cys¹⁶¹ pegylated Bacillus caldovelox arginase (BCA-PEG20) on colorectal cancer is determined as follows.

Athymic nude BALB/c mice (age of 6-8 weeks) are housed under sterile conditions with 12 hour light-dark cycle and provided with autoclaved feed and libitum. The mice are acclimated for at least 1 week before the start of experiments. Each nude mouse is implanted with about 3 mm³ of in vivo maintained HCT-15 human colorectal cancer cells to the right axilla subcutaneously. When stable palpable tumors of about 5 mm diameter are found, the mice are randomly separated into five different groups (Table 6). Intraperitoneal administrations of arginase drugs or control vehicle (PBS) are given twice per week while 5-fluorouracil is given once per week starting from Day 0. Tumor dimensions (L: longest diameter and W: its perpendicular diameter) and body weights are measured on every Monday, Wednesday and Friday with Vernier caliper. Tumor volume is calculated with the formula (½×L×W²) and number of fold increase in tumor volume (relative tumor volume) is calculated with reference to Day 0. The results are plotted against time. The mice are euthanized at the end of experiment or when tumor diameter reaches 2.5 cm.

TABLE 6 In vivo anti-tumor activity protocol Group Testing drug Units/mouse route Mice 1 PBS (control) N/A i.p. 4M 4F 2 Unpegylated Bacillus caldovelox 500 i.p. 4M 3F arginase 3 Cys¹⁶¹-pegylated Bacillus 250 i.p. 4M 3F caldovelox arginase 4 Cys¹⁶¹-pegylated Bacillus 250 i.p. 4M 3F caldovelox arginase + 5-Fluorouracil 5 5-Fluorouracil  10 mg/kg i.p. 2M 2F

No significant difference in average body weights between different groups is observed throughout the experiment and last recorded as 24.3±0.9 g for the control group, 22.1±1.0 g for the unpegylated Bacillus caldovelox arginase group, 24.2±0.7 g for the Cys¹⁶¹-pegylated Bacillus caldovelox arginase group, 23.5±1.2 g for the Cys¹⁶¹-pegylated Bacillus caldovelox arginase+5-fluorouracil group and 24.5±1.4 g for the 5-fluorouracil group at the end of experiment (FIG. 11D).

Both Cys¹⁶¹-pegylated Bacillus caldovelox arginase (BCA-PEG20) and unpegylated Bacillus caldovelox arginase (BCA) in all three arginase drugs treated groups suppress tumor growth with statistical significance (FIG. 12E and FIG. 12F). For the drug combination group (Cys¹⁶¹-pegylated Bacillus caldovelox arginase plus 5-fluorouracil), two-way ANOVA shows significance for number of folds of tumor volume and tumor volume with p<0.0001 in both cases. Bonferroni post-test further pinpoints the significant difference for number of folds of tumor volume to be from Day 36 to Day 40. For Cys¹⁶¹-pegylated Bacillus caldovelox arginase alone group, two-way ANOVA shows significance for number of folds of tumor volume and tumor volume with p=0.0005 and p=0.0011, respectively. Bonferroni post-test indicates the difference to be from Day 38 to Day 40 for number of folds of tumor volume and on Day 40 for tumor volume. For unpegylated Bacillus caldovelox arginase group, the p values for number of folds of tumor volume and tumor volume are 0.0202 and <0.0001, respectively. The 5-fluorouracil group does not show significant tumor suppression in terms of number of folds of tumor volume (FIG. 12F). The drug combination group results in statistically significant lower tumor volume and number of folds of tumor volume than both the Cys¹⁶¹-pegylated Bacillus caldovelox arginase alone group (p<0.0001 and p=0.0120, respectively) and the 5-fluorouracil alone group (p=0.0158 and p=0.0434, respectively). The results indicate a synergistic therapeutic effect for the Cys¹⁶¹-pegylated Bacillus caldovelox arginase and 5-fluorouracil.

In Vivo Inhibitory Efficacy on Breast Cancer Metastasis

1×10⁵ cells of a mouse metastatic breast cancer cell line (4T1) are injected orthotopically into the No. 4 inguinal mammary fat pad of wild-type BALB/c mice at the age of 6-8 weeks. When the tumors reach an average of 5 mm, the mice are divided into two different treatment groups (Table 7). BCA-PEG20 (250 U/mouse) or control vehicle (PBS) are injected intraperitoneally twice per week starting from Day 0. Body weight is measured every week. After three weeks, the mice are sacrificed and analyzed for the lung metastasis. The number of lung metastases are counted under a dissecting microscope after rinsing with PBS.

No significant difference in average body weight between different groups is observed throughout the experiment and last recorded as 21.8 g for control group and 21.5 g for the BCA-PEG20 group at the end of experiment.

Results demonstrate that BCA-PEG20 reduces the spontaneous lung tumor nodule formation compared with the PBS vehicle group. The spontaneous lung metastases are too numerous to count in PBS group but only 4 nodules on average are found in the BCA-PEG20 treatment group (Table 8). The result demonstrates that arginine depletion by BCA-PEG20 inhibits breast tumor metastasis.

TABLE 7 In vivo anti-metastasis protocol Group Testing drug Units/mouse route Mice 1 PBS (control) N/A i.p. 1M 2 BCA-PEG20 250 i.p. 2M

TABLE 8 Spontaneous Group Testing drug lung metastases 1 PBS (control) TNTC* 2 BCA-PEG20 4 *= Too numerous to count

Effect on HIV (HAI-PEG20)

The 50% inhibition concentration (IC₅₀) of the Cys⁴⁵ pegylated human arginase I (HAI-PEG20) on human immunodeficiency virus (HIV) is determined as a measurement of its effect on HIV.

The efficiency of an antiviral drug can be estimated using cell culture models for viral replication. The HIV replication assay utilizes H9 cells and HIV-1 strain RE H9 cells, derived from human T lymphocytes, are highly susceptible to infection by CXCR4-using HIV-1 isolates, and show clear signs of cytopathic effects a few days post infection. HIV-1 strain RF is a CXCR4-using class β isolate that replicates to high levels in H9 cells.

H9 cells are seeded in four 96-well plates at 5×10⁴ viable cells/mL and the cultures incubated at 37° C. The following day, two 96-well plates are inoculated with HIV-1 at 0.005 multiplicity of infection (50 μL per well).

Twenty-four hours after infection, the cells of one infected 96-well plate are treated with the Cys⁴⁵ pegylated human arginase I (HAI-PEG20) diluted to a final concentration of 1 U/mL, 10 U/mL and 50 U/mL in tissue culture medium (10% RPMI). Eight replicates are tested for each drug concentration and 100 μL is added per well.

Azido-thymidine (AZT) is used as a benchmark drug for this assay to ensure that a dose response is obtained. AZT is diluted appropriately (0.01, 0.1 and 1 μg/mL) in 10% RPMI and added to the second infected plate. Eight replicates are tested for each drug concentration and 100 μL is added per well.

A cytotoxicity control is set up in parallel: one 96-well plate of uninfected cells treated with three drug concentrations (1 U/mL, 10 U/mL and 50 U/mL; 8 replicates per drug concentration). This would allow the cytotoxic concentration to be determined (CC₅₀).

The remaining 96-well plate is inoculated with tissue culture medium alone to serve as the negative control.

Five days post infection plates are examined for cytopathic effect and the IC₅₀ of the drug is determined by comparing syncytial cell number in drug treated and non-treated cells.

The results show that H9 cells inoculated with HIV strain RF have viral infection, whereas H9 cells inoculated with tissue culture medium alone remain healthy throughout the study. Cytopathic effect is observed in the H9 cultures infected with HIV and treated with the Cys⁴⁵ pegylated human arginase I (HAI-PEG20) at all concentrations. Eight out of eight (8/8) infected wells treated with the pegylated enzyme at a final concentration of 1 U/mL display cytopathic effect. For infected wells treated with the enzyme at a final concentration of 10 U/mL, six out of eight (6/8) wells display cytopathic effect. When the drug is tested at the highest final concentration of 50 U/mL, three out of eight (3/8) wells display cytopathic effect. These results are shown in Table 9 and FIG. 13. The IC₅₀ of the drug is found to be approximately 37 U/mL.

When the benchmark drug AZT is added to infected wells at 0.01 μg/mL, seven out of eight (7/8) wells display cytopathic effect. For infected wells treated with AZT at 0.1 μg/mL, six out of eight (6/8) wells display cytopathic effect and when tested at 1 μg/mL, two out of eight (2/8) wells display cytopathic effect. These results are illustrated in FIG. 14. The IC₅₀ of the AZT is found to be 0.58 μg/mL.

TABLE 9 Virus inhibition assay Sample Results HIV without Cys⁴⁵ pegylated human arginase I treatment 24/24 HIV without Cys⁴⁵ pegylated human arginase I treatment 22/24 (second plate) HIV treated with Cys⁴⁵ pegylated human arginase I (50 U/mL) 3/8 HIV treated with Cys⁴⁵ pegylated human arginase I (10 U/mL) 6/8 HIV treated with Cys⁴⁵ pegylated human arginase I (1 U/mL) 8/8 HIV treated with AZT (0.01 μg/mL) 7/8 HIV treated with AZT (0.1 μg/mL) 6/8 HIV treated with AZT (1 μg/mL) 2/8 Negative control  0/96 Cytotoxicity control - uninfected cells treated with Cys⁴⁵  8/8* pegylated human arginase I (50 U/mL) Cytotoxicity control - uninfected cells treated with Cys⁴⁵  8/8* pegylated human arginase I (10 U/mL) Cytotoxicity control - uninfected cells treated with Cys⁴⁵  8/8* pegylated human arginase I (1 U/mL) Each well is inoculated with 50 μL of HIV at 0.005 multiplicity of infection. *= cytotoxicity observed in each well, therefore viability counts performed for 1 well for each concentration. The results are recorded as a ratio; e.g. 1/X, where 1 is the number of positive wells/number of wells inoculated.

Table 10 presents the viability counts for the cytotoxicity control. In the cytotoxicity test, all wells display symptoms of cytotoxicity, therefore viability counts are performed on one well for each concentration of Cys⁴⁵ pegylated human arginase I. The two highest concentrations, 50 U/mL and 10 U/mL, result in cell viabilities of 30% and 39%, respectively. For 1 U/mL, cell viability is 58%. Based on these results, cell viability is assessed for all 8 wells and the average is determined to be 48.9%. This approximates to a 50% reduction in cell viability based on the cell viability of cells (96.8%) when cells are seeded onto the 96 well plates. These results are displayed in Table 10 and FIG. 15, clearly demonstrating that HAI-PEG20 has inhibitory effects on HIV replication.

TABLE 10 Cell viability in cytotoxicity control Results Average % Sample Live cells Total cells % viability viability 50 U/mL - 1 well 9 30 30 N/A 10 U/mL - 1 well 11 28 39 N/A 1 U/mL well 1 19 33 58 well 2 30 63 48 well 3 23 59 39 48.9 well 4 21 60 35 well 5 33 58 57 well 6 29 56 52 well 7 31 49 63 well 8 24 61 39 N/A = not applicable

In Vitro Anti-Cancer Effects

In vitro cancer cell culture studies on the anti-cancer efficacies of different arginine-depleting enzymes are conducted for various cancer types.

Cell Proliferation Assay: For each cancer cell line, cells (5×10³) in 100 μL culture medium are seeded to the wells of a 96-well plate and incubated for 24 hours by standard method. The culture medium is replaced with medium containing different concentrations of one of the arginases of the present invention or wild type human arginase before genetic modification (rhArg) or arginine deiminase (ADI). The plates are incubated for an additional 3 days at 37° C. in an atmosphere of 95% air/5% CO₂. The metabolically viable cell fraction is determined by the MTT assay, which is performed to estimate the number of viable cells in the culture. Non-linear regression with Prism 4.0 (Graphpad Software) is used to fit a sigmoidal dose response curve, and the amount of each of the arginine-degrading enzymes (in terms of U/mL or unit/ml or μg/mL) needed to achieve 50% inhibition of cell growth is defined as IC₅₀.

RT-PCR studies: Total RNA is extracted from cancer cell lines grown in culture using the Qiagen RNeasy kit. For reverse transcription-polymerase chain reaction (RT-PCR), the RNA is first reverse-transcribed into cDNA by iScript cDNA Synthesis kit (Bio-Rad, CA) according to the manufacturer's instruction. Briefly, 5 μg of total RNA is subjected to reverse transcription (RT) at 42° C. for 30 min. A 2 μL portion of cDNA is then amplified using 50 μL of reaction mixture containing 0.5 units of iTaq DNA polymerase (Bio-Rad, CA). PCR is performed in a DNA thermal Mycycler (Bio-Rad, CA). The following flanking primers are used:

(a) Human ASS (448 bp product):

Sense: 5′-GGGGTCCCTGTGAAGGTGACC-3′; Anti-sense: 5′-CGTTCATGCTCACCAGCTC-3′

(b) Human ASL (218 bp product):

Sense: 5′- CTCCTGATGACCCTCAAGGGA -3′; Anti-sense: 5′-CATCCCTTTGCGGACCAGGTA-3′

(c) Human OTC (221 bp product):

Sense: 5′-GATTTGGACACCCTGGCTAA-3′; Anti-sense: 5′- GGAGTAGCTGCCTGAAGGTG-3′

(d) Human GAPDH (306 bp product):

Sense: 5′-AGCCACATCGCTCAGACA-3′; Anti-sense: 5′-GCCCAATACGACCAAATCC-3′

The reaction products are subjected to 1% agarose gel electrophoresis. After electrophoresis and staining with ethidium bromide, all PCR product band intensities are analyzed by Lumi-Imager (Boehringer Mannheim, Ind.), and the relative mRNA expression levels are estimated by normalization with the house keeping gene GADPH.

As the results indicate, arginases and ADI are all efficient arginine-degrading enzymes. Unexpectedly, all the cancer cell lines tested in this example are found to be sensitive to the arginases of the present invention but many cancer cell lines are actually resistant to ADI treatment. It is discovered in the present invention that this difference is due to the fact that the arginases of the present invention convert arginine to ornithine and urea while ADI converts it to citrulline and ammonia. Citrulline can be recycled back to arginine if the cancer cells are argininosuccinate synthetase (ASS)-positive and argininosuccinate lyase (ASL)-positive, leading to drug resistance. Most strikingly, if the cancer cells are ornithine transcarbamylase (OTC)-negative, they cannot recycle ornithine back to arginine in the cells even if they are ASS-positive and ASL-positive. This guideline provided by the present invention has been found to be consistent with all our data as well as data from other research groups. Under this guideline, for instance, if the cancer cells are either ASS-negative or ASL-negative or both, they would be arginase-sensitive and ADI-sensitive. On the other hand, if the cancer cells are both ASS-positive and ASL-positive but OTC-negative, they would be arginase-sensitive and ADI-resistant. Therefore, it is believed that the arginases of the present invention have broader anti-cancer applications than ADI. Furthermore, ammonia (product from ADI reaction) is more toxic than urea (product from arginase reaction). Thus, the arginases of the present invention serving as anti-cancer agents are believed to be safer than ADI.

In vitro anti-cancer efficacy results are summarized in Tables 11A-11G. As indicated in Table 11A, all the melanoma cell lines tested are sensitive to arginase treatments. When the arginases of the present invention are added to culture medium, arginine is converted to ornithine and urea. All these cells are OTC-negative and according to the guideline discussed above, these cells cannot recycle the arginase reaction product, ornithine, back to arginine in the cells, and therefore the cells are inhibited due to the lack of arginine. According to the IC₅₀ values, all the arginases tested are very effective on the inhibition of cancer cell growth.

Although all the melanoma cell lines tested are all ASS-positive and ASL-positive, the expression levels of ASS are low, which can be confirmed by performing an ASS activity assay. The low ASS expression level explains why these cell lines are all sensitive to ADI treatments. B16 is a mouse melanoma cell line and it is also sensitive to both arginases and ADI. Thus, it is believed that ADI killing the melanoma cells is due to the low level of ASS expression while the arginases of the present invention kill the melanoma cells because they are OTC-negative.

In Table 11B, it is shown that all the leukemia cell lines tested are sensitive to arginase treatments. Some of these cancer cells tested are OTC-negative and according to the guideline discussed above, these cells cannot recycle the arginase reaction product, ornithine, back to arginine in the cells, and therefore the cells are inhibited due to the lack of arginine. According to the IC₅₀ values, all the arginases tested are very effective on inhibition of leukemia cancer cell growth. For ADI treatments, all the 4 leukemia cell lines tested are sensitive except the RPMI8226 cell line which is resistant to ADI treatment, which is most likely due to the fact that it is both ASS-positive and ASL-positive. Therefore, for inhibiting leukaemia cells, the arginases are advantageous over ADI.

Table 11C shows that all the colorectal cancer cell lines tested are sensitive to arginase treatments. All these cancer cells tested are OTC-negative. In consistent with the guideline discussed above, these cells cannot recycle the arginase reaction product, ornithine, back to arginine in the cells, and therefore the cells are inhibited due to the lack of arginine. According to the IC₅₀ values, all the arginases tested are very effective on the inhibition of colorectal cancer cell growth. For ADI treatments, only 2 colorectal cancer cell lines (WiDr and HT29) tested are sensitive and the other 2 (SW1116 and HCT15) are resistant to ADI treatment, which is most likely due to the fact that they are both ASS-positive and ASL-positive. For HT29, although it is ASS-positive and ASL-positive according to the RT-PCR data, the expression level of ASS is relatively low, as confirmed by performing an ASS activity assay, which explains why this cell line is sensitive to ADI treatment.

Also shown in Table 11C, most strikingly, all the pancreatic cancer cell lines tested are sensitive to the arginase treatments. All these cancer cells tested are OTC-negative. As discussed above, these cells cannot recycle the arginase reaction product, ornithine, back to arginine in the cells, and therefore the cells are inhibited due to the lack of arginine. According to the IC₅₀ values, all the arginases tested are very effective on the inhibition of pancreatic cancer cell growth. For ADI treatments, only one pancreatic cancer cell line (Panc1) tested is sensitive and the other 2 (BxPC3 and HPAFII) are resistant to ADI treatment. Clearly, for inhibiting pancreatic cancer cells, arginases are better than ADI.

Table 11D shows that all the gastric cancer cell lines tested are sensitive to arginase treatments. All these cancer cells tested are OTC-negative and thus, as discussed above, these cells cannot recycle the arginase reaction product, ornithine, back to arginine in the cells, and therefore the cells are inhibited due to the lack of arginine. As the IC₅₀ values indicate, all the arginases tested are very effective on the inhibition of gastric cancer cell growth. In a sharp contrast, all the gastric cancer cell lines tested are resistant to ADI treatment, which is most likely due to the fact that they are both ASS-positive and ASL-positive. This similar result is obtained for the liver cancer (or HCC) cell lines tested as shown in Table 11E.

Table 11E also shows that the retinoblastoma cancer cell line Y79 tested is sensitive to arginase treatments but resistant to ADI treatment, which is most likely due to the fact that they are both ASS-positive and ASL-positive.

Table 11F shows that the lung cancer cell line A549 tested is sensitive to arginase treatments. These cancer cells tested are OTC-negative. It is also sensitive to ADI treatment, which is most likely due to the fact that they are either ASS-negative or ASL-negative. In contrast, also shown in Table 11F, all the cervical cancer cell lines tested are sensitive to arginase treatments (they are all OTC-negative), but only 2 cervical cancer cell line (SiHa and C-33A) tested are sensitive and the other 3 (HeLa, ME180, CC3) are resistant to ADI treatment, which is most likely due to the fact that they are both ASS-positive and ASL-positive.

The results for breast cancer cells are shown in Table 11G. As it is shown, all the breast cancer cell lines tested are sensitive to arginase treatments (they are all OTC-negative). Strikingly, only one breast cancer cell line (MDA-MB-231) tested is sensitive and the other 3 (MCF-7, ZR-75-1, Hs578T) are resistant to ADI treatments.

Also shown in Table 11G are results for the prostate cancer cell lines, which are found to be sensitive to both arginase and ADI treatments. As discussed above, such results can be explained by the fact that the cell lines are both OTC-negative and ASS-negative.

TABLE 11A Cell line name BCA HAI rhArg ADI Type of (medium, U/mL U/mL U/mL U/mL cancer source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL melanoma SK-mel-2 0.612 0.079 0.0556 0.0022 − − + + (EMEM (11.25) (0.80) (1.31) (0.082) L 10% FBS, 1% PS ATCC) SK-mel-24 0.204 0.012 − − + + (EMEM (4.82) (0.45) L 10% FBS, 1% PS NCI) SK-mel-28 0.91 0.064 0.0523 0.00084 − − + + (EMEM (16.72) (0.65) (1.233) (0.031) L 10% FBS, 1% PS ATCC) A375 0.15 0.061 0.0288 0.00059 − − + + (DMEM (2.76) (0.62) (0.679) (0.022) L 10% FBS, 1% PS ATCC) B16 0.02 0.004 − − + + (DMEM (0.48) (0.11) L 10% FBS, 1% PS ATCC)

TABLE 11B Cell line name BCA HAI rhArg ADI Type of (medium, U/mL U/mL U/mL U/mL cancer source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL leukemia HL60 0.03 0.016 + − − + (RPMI 10% FBS, (0.679) (0.591) 1% PS ATCC) K562 0.06 0.003 − − + − (RPMI 20% FBS, (1.357) (0.085) 1% PS ATCC) RPMI8226 0.09 R (RPMI 10% FBS, (2.036) 1% PS ATCC) Jurkat 0.41 0.037 0.002 (RPMI 10% FBS, (7.54) (0.86) (0.074) 1% PS ATCC)

TABLE 11C Cell line name BCA HAI rhArg ADI Type of (medium, U/mL U/mL U/mL U/mL cancer source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL colorectal (WiDr 0.215 0.075 0.038 0.035 + − + − DMEM (3.96) (0.76) (0.84) (0.9) 10% FBS, 1% PS ATCC) SW1116 1.417 0.41 0.15 R + − + + (RPMI (20.98) (4.18) (3.394) 10% FBS, 1% PS ATCC) HT29 0.231 0.03 0.032 + − + + (DMEM (4.24) (0.679) (0.83) L 10% FBS, 1% PS ATCC) HCT15 0.63 0.083 R + − + + (RPMI (6.44) (1.043) 10% FBS, 1% PS ATCC) pancreatic Panc1 0.263 0.09 0.049 − − + + (DMEM (4.84) (2.036) (1.39) L 10% FBS, 1% PS ATCC) BxPC3 0.846 0.08 R + − + + (EMEM (15.54) (1.809) 10% FBS, 1% PS ATCC) HPAFII 0.86 R − − + + (DMEM (19.35) 10% FBS, 1% PS ATCC)

TABLE 11D Cell line BCA HAI rhArg ADI Type of name (medium, U/mL U/mL U/mL U/mL cancer source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL gastric AGS 0.662 0.10 R − − + + (RPMI (12.17) (2.262) 10% FBS, 1% PS ATCC) MKN45 0.798 0.79 R − − + + (RPMI (14.67) (17.873) 10% FBS, 1% PS Riken Cell bank, Japan) BCG-823 0.11 R − − + + (RPMI (2.457) 10% FBS, 1% PS Beijing Institute of Cancer Research)

TABLE 11E Cell line BCA HAI rhArg ADI Type of name (medium, U/mL U/mL U/mL U/mL cancer source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL HCC PLC/PRF/5 2.376 0.94 0.312 R + − + + (liver (DMEM 10% FBS, (43.67) (9.56) (7.07) cancer) 1% PS ATCC) Hep3B 9.1 0.29 0.65 R + − + + (DMEM 10% FBS, (57.68) (2.95) (15.0) 1% PS ATCC) HepG2 2.002 0.097 0.177 R + − + + (DMEM 10% FBS, (36.79) (0.99) (4.00) 1% PS ATCC) Huh7 1.59 R + − + + (DMEM 10% FBS, (43) 1% PS ATCC) SK-HEP-1 12.27 1.725 0.15 0.007 − − + + (DMEM 10% FBS, (77.79) (6.05) (4) (0.2) L 1% PS ATCC) retinoblastoma Y79 0.5 R − − + + (RPMI 10% FBS, (11.3) 1% PS ATCC)

TABLE 11F BCA HAI rhArg ADI Type of Cell line name U/mL U/mL U/mL U/mL cancer (medium, source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL lung A549 0.3294 0.035 0.011 − − − + (DMEM 10% FBS, 1% PS (2.09) (0.44) (0.29) ATCC) Cervical HeLa 0.719 0.366 0.065 R − − + + (DMEM 10% FBS, 1% PS (13.21) (3.72) (0.82) ATCC) ME180 1.42 0.214 0.153 R − − + + (DMEM 10% FBS, 1% PS (26.16) (2.18) (1.93) ATCC) CC3 0.84 0.42 R − − + + (DMEM 10% FBS, 1% PS (15.50) (5.29) ATCC) SiHa 0.32 0.024 0.03 0.0025 − − − + (DMEM 10% FBS, 1% PS (5.84) (0.24) (0.38) (0.064) ATCC) C-33A 0.19 0.033 0.058 0.0014 − − − + (DMEM 10% FBS, 1% PS (3.55) (0.34) (0.72) (0.036) ATCC)

TABLE 11G BCA HAI rhArg ADI Type of Cell line name U/mL U/mL U/mL U/mL cancer (medium, source) (μg/mL) (μg/mL) (μg/mL) (μg/mL) ARG OTC ASS ASL breast MCF-7 0.05 0.28 R − − + + (EMEM 10% FBS, 1% PS (0.91) (6.36) ATCC) ZR-75-1 0.14 R − − + + (DMEM 10% FBS, 1% PS (3.18) ATCC) Hs578T 3.75 − + + (DMEM 10% FBS, 1% PS, (85.2) 10 μg/ml insulin NCI) MDA-MB-231 0.22 0.273 0.44 0.16 − − + + (DMEM 10% FBS, 1% PS (4.11) (10.0) (5.93) L NCI) 4T1 0.68 0.058 0.023 0.0007 (0.29) (0.017) Prostate PC3 0.263 0.40 0.08 0.0025 − − − + (DMEM 10% FBS, 1% PS (4.84) (4.07) (1.47) (0.064) ATCC) LNCap 2.119 0.47 0.41 0.13 (EMEM 10% FBS, 1% PS (38.94) (4.78) (5.16) (3.34) ATCC)

For Table 11A to Table 11G, “+”=mRNA is detected by RT-PCR, indicating the corresponding gene is expressed; “−”=mRNA is not detected by RT-PCR, indicating the gene is not expressed; “R” indicates that the cell line is ADI-resistant and the IC₅₀ value cannot be estimated; and “L” indicates that the cell line has a relatively low level of ASS expression and therefore the cell line is still ADI-sensitive.

While not wish to be bound by the following hypothesis and working models, it is believed that the following hypothesis and working models are consistent with the experimental data of the present invention and thus are useful guides for further utilization of the inventions disclosed herewith (also see FIG. 18).

Hypothesis and working model explaining why OTC-negative cancer cells are arginase-sensitive but can be ADI-resistant. When arginase is added in the culture medium or pegylated arginase is injected in the blood (in the body), arginine is converted into ornithine and urea by the arginase enzymatic reaction. Ornithine formed then passes into the cancer cells. Unlike normal cells, cancer cells grow rapidly and require much more arginine than normal cells for protein synthesis and other cellular processes. If the cancer cells are OTC-positive, ASS-positive and ASL-positive, ornithine can be recycled back into arginine. Therefore, cancer cells still have arginine and they are not arginine-deficient and cancer growth is not inhibited. On the other hand, cancer cells that are OTC-negative or ASS-negative or ASL-negative or any combination of these deficiencies or low expression level of any of these genes, the synthesis (or recycle) pathway from ornithine to arginine is blocked and therefore cancer cells are lack of arginine and cancer cell growth is thus inhibited and cancer cell death may occur.

Hypothesis and working model for liver cancer cells that are OTC-negative are also provided. The model relates to urea cycle gene expression and resistance towards pegylated arginine deiminase (ADI-PEG) and pegylated Bacillus caldovelox arginase (BCA-PEG20). Liver cancer cells express the urea cycle enzymes argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL) and arginase (ARG), but lack ornithine transcarbamylase (OTC). BCA-PEG20 in the bloodstream depletes arginine and produces ornithine, which enters the cell but fails to be recycled via the urea cycle owing to the absence of OTC. ADI-PEG converts arginine to citrulline, which can be readily converted back to arginine by ASS and ASL after uptake into liver cancer cells. Therefore, in this model, the liver cancer cells are sensitive to BCA-PEG20 treatment (inhibited by BCA-PEG20) but resistant to ADI-PEG treatment.

Hypothesis and working model for cancer cells that are OTC-negative are also provided. The model relates to gene expression in cancer cells and resistance towards pegylated arginine deiminase (ADI-PEG) and pegylated Bacillus caldovelox arginase (BCA-PEG20). For cancer cells that do not express arginase (ARG), cancer cells express the enzymes argininosuccinate synthetase (ASS), argininosuccinate lyase (ASL), but lack ornithine transcarbamylase (OTC). BCA-PEG20 in the bloodstream depletes arginine and produces ornithine, which enters the cell but fails to be recycled owing to the absence of OTC. ADI-PEG converts arginine to citrulline, which can be readily converted back to arginine by ASS and ASL after uptake into the cancer cells. Therefore, in this model, the cancer cells are sensitive to BCA-PEG20 treatment (inhibited by BCA-PEG20) but resistant to ADI-PEG treatment. This model can be applied to cancer cells in general.

Method of Further Enhancing Arginase Activity by Using Cobalt as Metal Cofactor

The native metal cofactor of arginase is manganese (Mn²⁺). It is surprisingly discovered by the present invention that replacing the manganese with cobalt dramatically enhances the enzyme's activity. Either Bacillus caldovelox arginase (BCA) or the human arginase I (HAI) is expressed as described previously. The purification method is the same as described before except 10 mM of metal ion (CoSO₄ or MnSO₄) is added into the purified protein elution from Nickel affinity chromatography instead of added before Nickel affinity chromatography. Eluted factions containing the arginase enzyme are incubated with 10 mM metal for 15 min at 50-55° C., followed by filtration through a 0.45 μm syringe filter. Then the solution is exchanged with storage buffer by ultrafiltration.

Diacetylmonoxine (DAMO) assay is used to determine the kinetic parameters of human arginase I with different metal cofactors. All enzymatic reactions are carried out at pH 7.4. The results are shown in FIG. 16. The steady-state kinetics of human arginase I (HAI) substituted with Mn²⁺ or Co²⁺ are measured in sodium phosphate buffer pH 7.4, 25° C. The K_(m) of HAI with Mn²⁺ (HAI Mn²⁺) and HAI with Co²⁺ (HAI Co²⁺) are 1.83 mM and 0.19 mM respectively. Since the Km value is improved about 10-fold in HAI Co²⁺, its specific activity is improved 10-fold and is a much more efficient drug to deplete arginine than HAI Mn²⁺.

Enhancing Arginase Activity by Further Genetic Modification

To determine if modifying the amino acid residues around the active bind site of arginase would enhance its enzymatic activity, the amino acid residues at positions 15, 20, 102, 123, 127, 132, 133, 134, 137, 140, 141, 142, 143, 171, 174, 176, 177, 185, 224, 238, 240, 242 and 270 of Cys¹⁶¹ Bacillus caldovelox arginase are further mutated and replaced with other amino acid residues as shown in Table 12. The mutants are cloned, their enzymatic activities are measured and compared with Cys¹⁶¹ Bacillus caldovelox arginase. Among all mutants, only 9 of them show an increase in enzymatic activity when compared with BCA before modification, they are V205, V20G, V20P, V127S, M141L, M141A, L171F, I185V and V238T (Table 13).

TABLE 12 Original amino acid Position residue Amino acid residues replaced 1 15 Q K, N, M, I, T, R, S, Q, H, L, P, E, D, V, A, G 2 20 V S, I, T, R, L, P, G, V, A 3 102 A S, I, T, R, L, P, G, V, A, C, F 4 123 A S, T, G, A 5 127 V R, S, M, I, T, W, C, L, F, S, R, L, P 6 132 T K, N, M, I, T, R, S, Q, H, L, P, R, E, D, V, A, G 7 133 S T 8 134 P S, I, T, G, V, A 9 137 N Q 10 140 G A 11 141 M S, I, T, R, L, P, G, V, A 12 142 P S, I, T, R, L, P, G, V, A, C, F 13 143 L S, I, T, R, L, P, G, V, A, C, F 14 171 L S, I, T, R, L, P, G, V, A, C, F 15 174 V T, M, I, P, L, V 16 176 S K, N, I, T, Q, H, L, P, E, D, V, A 17 177 L T, I, P, L, A, V 18 185 I D, V, A, Y, F, S, H, L, P 19 224 S G, A, C, S 20 238 V T, I, P, L, A, V 21 240 T D, A, G, N, T, S, Y, C 22 242 V S, I, T, R, L, P, G, V, A 23 270 V S, I, T, R, L, P, G, V, A

TABLE 13 Clone Enzymatic Activity BCA before modification ++ V20S ++++ V20G ++++ V20P +++++ V127S +++ M141L +++ M141A ++++ L171F +++ I185V +++ V238T +++

As shown in Table 13, it is surprisingly discovered by the present invention that the position 20 of BCA can be substituted with valine to improve enzyme activity, the mutated strain is referred to as “BCA mutant V20P”. Steady-state kinetics of the BCA mutant V20P and BCA with Mn²⁺ or Co²⁺ are measured in sodium phosphate buffer pH 7.4, 25° C. and are shown in FIG. 17. The Km values of BCA mutant V20P with Mn²⁺ and BCA mutant V20P with Co²⁺ are about 1.29 mM and 0.18 mM respectively. The Km of BCA with Mn²⁺ is about 3.2 mM. Therefore, the BCA mutant V20P with Co²⁺ as cofactor (Km=0.18 mM) is a much more efficient drug to deplete arginine than the BCA with Mn²⁺ (Km=3.2 mM).

In Vitro Cancer Cell Line Studies Using BCA Mutant V20P

Cell proliferation assay is conducted as follows.

2.5×10³ SK-MEL-28 (EMEM), 5×10³ HEK293 (EMEM), MCF-7 (EMEM), HCT-15 (RPMI), Hep3B (DMEM), PANC-1 (DMEM), Hela (DMEM) and A549 (DMEM) cells are seeded to each well of a 96-well plate in 100 μL culture medium and are allowed to adhere to the plate overnight. On the next day, the culture medium is replaced with medium containing different concentrations of BCA and BCA mutant V20P protein drug. 2×10⁴ Jurkat (RPMI) floating cells are seeded to each well of a 96-well plate in 50 μL culture medium at the day of adding protein drug and different concentrations of protein drug in 50 μL are added directly to each well. The cells are allowed to incubate for an additional 3 days at 37° C. in an atmosphere of 95% air/5% CO₂. MTT cell proliferation assay (Invitrogen) is then performed to estimate the number of viable cells in the culture. In brief, 10 μL of 5 mg/mL water-soluble MTT reagent is added to 100 μL culture medium and incubated at 37° C. for 4 hours. MTT is chemically reduced by cells into purple formazan, which is then dissolved by acidified SDS (0.01 N HCl in 10% SDS) in tissue culture medium. Concentration of the cleavage product formazan is then measured by reading its absorbance with a spectrophotometer with a 570 nm filter. Cell proliferation data are expressed as a percentage of control. Non-linear regression is used to fit a sigmoidal dose response curve with Prism 4.0 (Graphpad Software), and the amount of protein drug needed to achieve 50% cell growth inhibition is defined as IC₅₀. The results are shown in Table 14. The corresponding enzymatic activities are shown in Table 15.

TABLE 14 IC₅₀ of BCA and BCA mutant V20P in different kinds of cancer cells IC₅₀ Value Fold of Difference BCA (BCA/BCA BCA mutant V20P mutant V20P) (U/mL) (mg/mL) (U/mL) (mg/mL) (U/mL) (mg/mL) HCT-15 Colon 15.62 0.0916 7.34 0.0132 2.13 6.96 Jurkat Leukemia 6.84 0.0401 0.90 0.0016 7.60 24.85 MCF-7 Breast 5.51 0.0323 2.87 0.0051 1.92 6.28 SK-MEL- Melanoma 3.35 0.0197 1.52 0.0027 2.20 7.21 28 HEK293 Kidney 3.86 0.0226 3.40 0.0061 1.14 3.71 A549 Lung 2.67 0.0157 1.64 0.0029 1.63 5.32 Hep3B Liver 9.42 0.0552 9.43 0.0169 1.00 3.27 Hela Cervical 2.83 0.0166 1.37 0.0025 2.07 6.75 PANC-1 Pancreatic 1.20 0.0070 0.87 0.0016 1.38 4.51

TABLE 15 Specific activity of the proteins Protein concentration Specific activity Enzyme activity (mg/mL) (U/mg) (U/mL) BCA 3.046 170.47 519.3 BCA mutant 2.63 557.3 1465.7 V20P

Pegylation of BCA Mutant V20P

BCA mutant V20P is pegylated with a single chain mPEG-maleimide (20 kDa), referred to as “BCA-V20P-PEG20”. The double bond of a maleimide undergoes an alkylation reaction with a sulfhydryl group to form a stable thioether bond. One gram of BCA mutant V20P is diafiltered into 0.02 M sodium phosphate, 0.5 M NaCl, pH 7.4, using Millipore Tangential Flow Filtration system (500 mL) with 10 K (cut-off) membrane (Millipore). The concentration of arginase is finally diluted to about 2 mg/mL. The reducing agent Tris(2-carboxyethyl)phosphine, TCEP, is added in a molar excess of 10 moles to one mole of arginase for reduction and the solution is gently stirred for 4 hours at room temperature. mPEG-Maleimide or mPEG-MAL (20 kDa) (Sunbright) in a molar excess of 20 moles to one mole of arginase is added to the reduced arginase and stirred for overnight at 4° C. The progress of site-directed pegylation is monitored by SDS-PAGE (FIG. 23). Under the above described conditions, the free sulfhydryl group of cysteine at position 161 on BCA mutant V20P is specifically linked via a stable thioether bond to the activated maleimide group of mPEG-MAL (20 kDa). Enzymatic activity of unpegylated BCA mutant V20P and Cys¹⁶¹ pegylated BCA mutant V20P are measured and shown in Table 16.

TABLE 16 Specific activity (U/mg) Unpegylated BCA mutant V20P 566.58 Cys¹⁶¹ pegylated BCA mutant V20P 499.41

The results show that BCA mutant V20P is much more efficient in killing various types of cancer cells in in vitro drug efficacy studies and can be pegylated without significant loss of activity

While there have been described and pointed out fundamental novel features of the invention as applied to a preferred embodiment thereof, it will be understood that various omissions and substitutions and changes, in the form and details of the embodiments illustrated, may be made by those skilled in the art without departing from the spirit of the invention. The invention is not limited by the embodiments described above which are presented as examples only but can be modified in various ways within the scope of protection defined by the appended patent claims. 

What is claimed is:
 1. A pharmaceutical composition for treating an arginine-dependent disease comprising a polyethylene glycol-arginase conjugate having a polyethylene glycol moiety covalently attached to a genetically-modified Bacillus caldovelox arginase or a genetically-modified arginase of other species, the genetic modification being such that one or two cysteine residues are substituted at one or two positions at a distance located away from the active binding site of the arginase such that the covalently bound polyethylene glycol moiety at the one or two cysteine residues preserves the binding activity of the active binding site the molecular weight of the polyethylene glycol moiety is 10,000-30,000 Da, the polyethylene glycol moiety being bound at the introduced cysteine residues and being substantially not bound at other locations on the genetically-modified Bacillus caldovelox arginase or the genetically-modified arginase of other species.
 2. The pharmaceutical composition of claim 1 wherein said arginase of other species is a genetically-modified arginase derived from a species comprising Bacillus methanolicus, Bacillus sp. NRRL B-14911, Planococcus donghaensis, Paenibacillus dendritiformis, Desmospora sp., Methylobacter tundripaludum, Stenotrophomonas sp., Microbacterium laevaniformans, Porphyromonas uenonis, Agrobacterium sp., Octadecabacter arcticus, Agrobacterium tumefaciens, Anoxybacillus flavithermus, Bacillus pumilus, Geobacillus thermoglucosidasius, Geobacillus the rmoglucosidans, Brevibacillus laterosporus, Desulfotomaculum ruminis, Geobacillus kaustophilus, Geobacillus thermoleovorans, Geobacillus thermodenitrificans, Staphylococcus aureus, Halophilic archaeon DL31, Halopiger xanaduensis and Natrialba magadii.
 3. The pharmaceutical composition of claim 1 further comprising a therapeutic agent for treating an arginine-dependent disease.
 4. The pharmaceutical composition of claim 2 wherein the therapeutic agent is for treating cancer.
 5. The pharmaceutical composition of claim 1 wherein the polyethylene glycol is a single chain or branched chain polyethylene glycol.
 6. A pharmaceutical composition for treating an arginine-dependent disease comprising a polyethylene glycol-arginase conjugate having a polyethylene glycol moiety covalently attached to a genetically-modified human arginase or a genetically-modified arginase of other species, the genetic modification being such that one or two cysteine residues are retained at one or two positions at a distance located away from the active binding site of the arginase while other redundant cysteine residues of the arginase are removed such that the covalently bound polyethylene glycol moiety at each of the retained one or two cysteine residues preserves the binding activity of the active binding site, the molecular weight of the polyethylene glycol moiety being 10,000-30,000 Da, the polyethylene glycol moiety being bound at each of the retained one or two cysteine residues and being substantially not bound at other locations on the genetically-modified human arginase or the genetically-modified arginase of other species.
 7. The pharmaceutical composition of claim 6 wherein said arginase of other species is a genetically modified arginase derived from a species comprising Capra hircus, Heterocephalus glaber, Bos taurus, Sus scrofa, Plecoglossus altivelis, Salmo salar, Oncorhynchus mykiss, Osmerus mordax, Hyriopsis cumingii, Rattus norvegicus, Mus musculus, Pan troglodytes, Oryctolagus cuniculus, Delftia, Bacillus coagulans, Hoeflea phototrophica and Roseiflexus castenholzii.
 8. The pharmaceutical composition of claim 6 further comprising a therapeutic agent for treating an arginine-dependent disease.
 9. The pharmaceutical composition of claim 8 wherein the therapeutic agent is for treating cancer.
 10. The pharmaceutical composition of claim 6 wherein the polyethylene glycol is a single chain or branched chain polyethylene glycol.
 11. A pharmaceutical composition for treating an arginine-dependent disease comprising a polyethylene glycol-arginase conjugate having a polyethylene glycol moiety covalently attached to one or more lysine residues in Bacillus caldovelox arginase or attached to one or more lysine residues in Bacillus caldovelox arginase that have been genetically modified to substitute one or more cysteine residues for the one or more lysine residues the covalently bound polyethylene glycol moieties preserving the binding activity of the active binding site, the molecular weight of the polyethylene glycol moiety being 10,000-30,000 Da, the polyethylene glycol moiety being bound at the lysine or substituted lysine residues and being substantially not bound at other locations on the Bacillus caldovelox arginase.
 12. The pharmaceutical composition of claim 11 further comprising a therapeutic agent for treating an arginine-dependent disease.
 13. The pharmaceutical composition of claim 12 wherein the therapeutic agent is for treating cancer.
 14. The pharmaceutical composition of claim 11 wherein the polyethylene glycol is a single chain or branched chain polyethylene glycol.
 15. The pharmaceutical composition of claim 1, wherein a native valine residue at position 20 of said genetically modified Bacillus caldovelox arginase is further replaced by proline in order to enhance enzymatic activity of said arginase.
 16. The pharmaceutical composition of claim 6, wherein a native valine residue of said genetically-modified human arginase or arginase of other species which is equivalent to a native valine residue at position 20 of a Bacillus caldovelox arginase is further replaced by proline in order to enhance enzymatic activity of said human arginase.
 17. The pharmaceutical composition of claim 1, wherein a native metal cofactor manganese of said genetically-modified Bacillus caldovelox arginase is further replaced by cobalt or other metal ions in order to enhance enzymatic activity of said arginase.
 18. The pharmaceutical composition of claim 6, wherein a native metal cofactor manganese of said human arginase is further replaced by cobalt or other metal ions in order to enhance enzymatic activity of said arginase.
 19. The pharmaceutical composition of claim 1 is administrated in combination with an anti-neoplastic compound to a subject in needs thereof for treating an arginine-dependent disease, wherein said subject is an animal including human.
 20. The pharmaceutical composition of claim 6 is administrated in combination with an anti-neoplastic compound to a subject in needs thereof for treating an arginine-dependent disease, wherein said subject is an animal including human. 